Doxygen: Fix Diags, FieldSolver, Parallelization & Particles (#2662)

* Doxygen: Fix Diags, FieldSolver, Parallelization & Particles

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Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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9 files changed, 22 insertions, 0 deletions

diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/ComovingPsatdAlgorithm.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/ComovingPsatdAlgorithm.H
index b6d46095e..a1e4a4412 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/ComovingPsatdAlgorithm.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/ComovingPsatdAlgorithm.H
@@ -55,6 +55,7 @@ class ComovingPsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -71,6 +72,7 @@ class ComovingPsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.H
index 0907cf37f..10ad6dbc5 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.H
@@ -35,6 +35,7 @@ class GalileanPsatdAlgorithmRZ : public SpectralBaseAlgorithmRZ
          * base class \c SpectralBaseAlgorithmRZ (qualifier \c override) and cannot be
          * overridden by further derived classes (qualifier \c final).
          *
+         * \param[in]     lev        mesh-refinement level
          * \param[in,out] field_data all fields in Fourier space
          * \param[in,out] current    two-dimensional array of unique pointers to MultiFab
          *                           storing the three components of the current density
@@ -51,6 +52,7 @@ class GalileanPsatdAlgorithmRZ : public SpectralBaseAlgorithmRZ
          * base class \c SpectralBaseAlgorithmRZ and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PMLPsatdAlgorithm.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PMLPsatdAlgorithm.H
index ce71d5a37..d6d7e074e 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PMLPsatdAlgorithm.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PMLPsatdAlgorithm.H
@@ -52,6 +52,7 @@ class PMLPsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -69,6 +70,7 @@ class PMLPsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithm.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithm.H
index 954c313ee..41053fc9e 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithm.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithm.H
@@ -38,12 +38,15 @@ class PsatdAlgorithm : public SpectralBaseAlgorithm
          * \param[in] norder_y order of the spectral solver along y
          * \param[in] norder_z order of the spectral solver along z
          * \param[in] nodal whether the E and B fields are defined on a fully nodal grid or a Yee grid
+         * \param[in] fill_guards Update the guard cells (in addition to the valid cells) when pushing the fields in time
          * \param[in] v_galilean Galilean velocity (three-dimensional array)
          * \param[in] dt time step of the simulation
          * \param[in] update_with_rho whether the update equation for E uses rho or not
          * \param[in] time_averaging whether to use time averaging for large time steps
          * \param[in] J_linear_in_time whether to use two currents computed at the beginning and the end
          *            of the time interval (instead of using one current computed at half time)
+         * \param[in] dive_cleaning Update F as part of the field update, so that errors in divE=rho propagate away at the speed of light
+         * \param[in] divb_cleaning Update G as part of the field update, so that errors in divB=0 propagate away at the speed of light
          */
         PsatdAlgorithm (
             const SpectralKSpace& spectral_kspace,
@@ -114,6 +117,7 @@ class PsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -132,6 +136,7 @@ class PsatdAlgorithm : public SpectralBaseAlgorithm
          * base class \c SpectralBaseAlgorithm and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithmRZ.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithmRZ.H
index 77f33c631..a23afbf4c 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithmRZ.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithmRZ.H
@@ -38,6 +38,7 @@ class PsatdAlgorithmRZ : public SpectralBaseAlgorithmRZ
          * base class \c SpectralBaseAlgorithmRZ and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -55,6 +56,7 @@ class PsatdAlgorithmRZ : public SpectralBaseAlgorithmRZ
          * base class \c SpectralBaseAlgorithmRZ and cannot be overridden by further
          * derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithm.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithm.H
index ad9f9925e..1efaf8319 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithm.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithm.H
@@ -48,6 +48,7 @@ class SpectralBaseAlgorithm
          * (<a href="https://doi.org/10.1016/j.jcp.2013.03.010"> Vay et al, 2013</a>).
          * This virtual function is pure and must be defined in derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -63,6 +64,7 @@ class SpectralBaseAlgorithm
          * (<a href="https://doi.org/10.1016/j.jcp.2013.03.010"> Vay et al, 2013</a>).
          * This virtual function is pure and must be defined in derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithmRZ.H b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithmRZ.H
index a494a3291..61b877c3e 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithmRZ.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/SpectralBaseAlgorithmRZ.H
@@ -33,6 +33,7 @@ class SpectralBaseAlgorithmRZ
          * (<a href="https://doi.org/10.1016/j.jcp.2013.03.010"> Vay et al, 2013</a>).
          * This virtual function is pure and must be defined in derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
@@ -55,6 +56,7 @@ class SpectralBaseAlgorithmRZ
          * (<a href="https://doi.org/10.1016/j.jcp.2013.03.010"> Vay et al, 2013</a>).
          * This virtual function is pure and must be defined in derived classes.
          *
+         * \param[in]     lev        The mesh-refinement level
          * \param[in,out] field_data All fields in Fourier space
          * \param[in,out] current    Array of unique pointers to \c MultiFab storing
          *                           the three components of the current density
diff --git a/Source/FieldSolver/SpectralSolver/SpectralSolver.H b/Source/FieldSolver/SpectralSolver/SpectralSolver.H
index b2a33c323..5c3036838 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralSolver.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralSolver.H
@@ -47,6 +47,7 @@ class SpectralSolver
          * \param[in] norder_y spectral order along y
          * \param[in] norder_z spectral order along z
          * \param[in] nodal whether the spectral solver is applied to a nodal or staggered grid
+         * \param[in] fill_guards Update the guard cells (in addition to the valid cells) when pushing the fields in time
          * \param[in] v_galilean three-dimensional vector containing the components of the Galilean
          *                       velocity for the standard or averaged Galilean PSATD solvers
          * \param[in] v_comoving three-dimensional vector containing the components of the comoving
@@ -123,6 +124,7 @@ class SpectralSolver
          * by its derived classes (e.g. PsatdAlgorithm, GalileanAlgorithm), from
          * objects of class SpectralSolver through the private unique pointer \c algorithm
          *
+         * \param[in]     lev     The mesh refinement level
          * \param[in,out] current three-dimensional array of unique pointers to MultiFab
          *                        storing the three components of the current density
          * \param[in]     rho     unique pointer to MultiFab storing the charge density
@@ -139,6 +141,7 @@ class SpectralSolver
          * derived classes, from objects of class SpectralSolver through the private
          * unique pointer \c algorithm.
          *
+         * \param[in]     lev     The mesh refinement level
          * \param[in,out] current Array of unique pointers to \c MultiFab storing
          *                        the three components of the current density
          */
diff --git a/Source/FieldSolver/SpectralSolver/SpectralSolverRZ.H b/Source/FieldSolver/SpectralSolver/SpectralSolverRZ.H
index 52f422799..b97487401 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralSolverRZ.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralSolverRZ.H
@@ -98,6 +98,7 @@ class SpectralSolverRZ
          * by its derived classes (e.g. PsatdAlgorithmRZ), from
          * objects of class SpectralSolverRZ through the private unique pointer \c algorithm
          *
+         * \param[in]     lev     The mesh refinement level
          * \param[in,out] current two-dimensional array of unique pointers to MultiFab
          *                        storing the three components of the current density
          * \param[in]     rho     unique pointer to MultiFab storing the charge density
@@ -111,6 +112,7 @@ class SpectralSolverRZ
          * derived classes, from objects of class SpectralSolverRZ through the private
          * unique pointer \c algorithm.
          *
+         * \param[in]     lev     The mesh refinement level
          * \param[in,out] current Array of unique pointers to \c MultiFab storing
          * the three components of the current density
          */